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chore: prepare for release #88

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merged 5 commits into from
Nov 6, 2024
Merged

chore: prepare for release #88

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afa1e58
chore: update modules
znorgaard Oct 31, 2024
cd6abe7
chore: bump version to 1.0.2
znorgaard Oct 31, 2024
6d26488
chore: update changelog
znorgaard Oct 31, 2024
d796af3
chore: update snapshot
znorgaard Oct 31, 2024
5bc7de7
chore: fix release date
znorgaard Nov 6, 2024
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2 changes: 1 addition & 1 deletion .nf-core.yml
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Expand Up @@ -23,5 +23,5 @@ template:
org: nf-core
outdir: .
skip_features: null
version: 1.0.2dev
version: 1.0.2
update: null
9 changes: 8 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -3,14 +3,21 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## Unreleased
## [[1.0.2]](https://github.com/nf-core/fastquorum/releases/tag/1.0.2) -- 2024-10-31

### Enhancements & fixes

- [PR #87](https://github.com/nf-core/fastquorum/pull/87) - Raise minimum version to 24.04.2
- [PR #84](https://github.com/nf-core/fastquorum/pull/84) - Update to nf-core/tools template version 3.0.2
- [PR #79](https://github.com/nf-core/fastquorum/pull/79) and [PR #80](https://github.com/nf-core/fastquorum/pull/90) - Publish aligned consensus bai file

### Credits

Special thanks to the following for their contributions to the release:

- [Simon Pearce](https://github.com/SPPearce)
- [Zach Norgaard](https://github.com/znorgaard)

## [[1.0.1]](https://github.com/nf-core/fastquorum/releases/tag/1.0.1) -- 2024-09-10

### Credits
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4 changes: 2 additions & 2 deletions assets/multiqc_config.yml
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@@ -1,7 +1,7 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/fastquorum/tree/dev" target="_blank">nf-core/fastquorum</a>
This report has been generated by the <a href="https://github.com/nf-core/fastquorum/releases/tag/1.0.2" target="_blank">nf-core/fastquorum</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/fastquorum/dev/docs/output" target="_blank">documentation</a>.
<a href="https://nf-co.re/fastquorum/1.0.2/docs/output" target="_blank">documentation</a>.
report_section_order:
"nf-core-fastquorum-methods-description":
order: -1000
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4 changes: 2 additions & 2 deletions modules.json
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Expand Up @@ -46,7 +46,7 @@
"nf-core": {
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
"git_sha": "56372688d8979092cafbe0c5c3895b491166ca1c",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
Expand All @@ -56,7 +56,7 @@
},
"utils_nfschema_plugin": {
"branch": "master",
"git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
"git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
"installed_by": ["subworkflows"]
}
}
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -241,7 +241,7 @@ manifest {
description = """fgbio Best Practices FASTQ to Consensus Pipeline"""
mainScript = 'main.nf'
nextflowVersion = '!>=24.04.2'
version = '1.0.2dev'
version = '1.0.2'
doi = '10.5281/zenodo.10456900,10.5281/zenodo.11267672'
}

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10 changes: 6 additions & 4 deletions subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
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Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

4 changes: 2 additions & 2 deletions subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
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Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
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Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

4 changes: 2 additions & 2 deletions tests/pipeline/multi_fastq.nf.test.snap
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Expand Up @@ -16,7 +16,7 @@
},
"multi_fastq_ht_software_versions": {
"content": [
"{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2dev}}"
"{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2}}"
],
"meta": {
"nf-test": "0.8.4",
Expand All @@ -26,7 +26,7 @@
},
"multi_fastq_rd_software_versions": {
"content": [
"{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2dev}}"
"{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2}}"
],
"meta": {
"nf-test": "0.8.4",
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14 changes: 7 additions & 7 deletions tests/pipeline/multi_lanes.nf.test.snap
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@@ -1,13 +1,13 @@
{
"multi_lanes_rd_software_versions": {
"content": [
"{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, MERGE_BAM={samtools=1.2}, SORTBAM={fgbio=2.2.1}, Workflow={nf-core/fastquorum=v1.0.2dev}}"
"{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, MERGE_BAM={samtools=1.21}, SORTBAM={fgbio=2.2.1}, Workflow={nf-core/fastquorum=v1.0.2}}"
],
"meta": {
"nf-test": "0.8.4",
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-23T11:44:11.374426"
"timestamp": "2024-10-31T14:39:27.884022"
},
"multi_lanes_ht": {
"content": [
Expand All @@ -26,13 +26,13 @@
},
"multi_lanes_ht_software_versions": {
"content": [
"{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, MERGE_BAM={samtools=1.2}, SORTBAM={fgbio=2.2.1}, Workflow={nf-core/fastquorum=v1.0.2dev}}"
"{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, MERGE_BAM={samtools=1.21}, SORTBAM={fgbio=2.2.1}, Workflow={nf-core/fastquorum=v1.0.2}}"
],
"meta": {
"nf-test": "0.8.4",
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-23T11:47:27.269353"
"timestamp": "2024-10-31T14:42:58.125095"
},
"multi_lanes_rd": {
"content": [
Expand All @@ -49,4 +49,4 @@
},
"timestamp": "2024-05-20T01:34:44.993842"
}
}
}
4 changes: 2 additions & 2 deletions tests/pipeline/single_fastq.nf.test.snap
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Expand Up @@ -11,7 +11,7 @@
},
"single_fastq_ht_software_versions": {
"content": [
"{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERMOLECULARCONSENSUSREADS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2dev}}"
"{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERMOLECULARCONSENSUSREADS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2}}"
],
"meta": {
"nf-test": "0.8.4",
Expand All @@ -21,7 +21,7 @@
},
"single_fastq_rd_software_versions": {
"content": [
"{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLMOLECULARCONSENSUSREADS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2dev}}"
"{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLMOLECULARCONSENSUSREADS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2}}"
],
"meta": {
"nf-test": "0.8.4",
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4 changes: 2 additions & 2 deletions tests/pipeline/tiny.nf.test.snap
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@@ -1,7 +1,7 @@
{
"tiny_rd_software_versions": {
"content": [
"{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2dev}}"
"{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2}}"
],
"meta": {
"nf-test": "0.8.4",
Expand All @@ -11,7 +11,7 @@
},
"tiny_ht_software_versions": {
"content": [
"{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2dev}}"
"{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2}}"
],
"meta": {
"nf-test": "0.8.4",
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